title: MNaseH3_CTCFAID_M_plusIAA_2

data_processing:
Library strategy: MNase H3 ChIP-seq
ChIP-seq: Reads aligned with Bowtie2 with options “-k 10”. Reads were filtered for mapping quality 255 and edit distance <= 4. Reads with identical barcode, alignment position & strand  were treated as PCR-duplicates and collapsed. Peaks called with MACS2 with options “callpeak -q 0.2 -g mm”. BigWig files were generated by extending reads to mean fragment length.
Mnase-seq & MINCE-seq: Paired end reads were trimmed by alignment for reverse complementary regions surrounded by relevant adapters. Reads were aligned using Bowtie2 with options “-k 10 -I 0 -X 1000 --no-discordant --no-mixed”. Pairs were filtered for mapping quality 255 and mean edit-distance <= 4. BigWig files were generated by marking the +/-20bp of the midpoint of fragments in [140, 200]bp.
Genome_build: mm10
Supplementary_files_format_and_content: BigWigFiles

value: CTCFAID

tag: chip antibody

value: Histone H3 (Abcam ab1791)

value: plusIAA


title: Ccrescentus_wt_rep3

status: Public on Nov 05 2019

type: RNA

city: Lausanne

first: Diego

last: Gonzalez

address: Quartier UNIL-Sorge, Bâtiment Biophore

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

hyb_protocol: Roche / NimbleGen protocol

scan_protocol: Scanning with an Agilent microarray scanner at 3 μm resolution

data_processing: Normalization with Nimblescan implemented RMA algorithm over the whole chip.

molecule: total RNA

organism: Caulobacter vibrioides NA1000

source_name: Bacterial cells_WT

label_protocol: Roche / NimbleGen Cy3 labelling protocol

growth_protocol: Biological triplicates of NA1000 vs NA1000-ΔcdnL grown in PYE at 28°C with agitation

extract_protocol: Trizol / Ambion RNA extraction kit

treatment_protocol: RNA extracted from 2 x 1ml OD660=0.3 for each replicate

tag: genotype/variation

value: wild-type


title: MNaseH3_CTCFAID_I_plusIAA_2

type: SRA

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cell

growth_protocol: ES cells (wild-type E14Tg2a and CTCF-aid derivatives) were cultured on 0.1% gelatine (SIGMA, G1890-100G) in DMEM+GlutaMax-I (Gibco, 31966-021), 10% FCS (Gibco 10270- 098), 100μM β-mercaptoethanol (Gibco, 31350-010), 1×MEM non-essential amino acids (Gibco, 1140-035) and 10ng/ml recombinant LIF (MILTENYI BIOTEC, 130-099-895). ES cells were passaged 1:10 every 2–3 days. NIH3T3 and C2C12 cells were cultured in DMEM + GlutaMax-I supplemented with 10% FCS. NIH3T3 and C2C12 were passaged 1:15 and 1/20, respectively, every 3 days.

extract_protocol: ChIP-seq/Mnase-seq: For interphase, 2.5x106 fixed cells (1% formaldehyde for 10min followed by 5min with 0.125 M Glycine) were resuspended in 2ml swelling buffer (25mM Hepes pH 7.95, 10mM KCl, 10mM EDTA; freshly supplemented with 1× protease inhibitor cocktail – 04 693 116 001 PIC-Roche, and 0.5% IGEPAL), incubated for 30min on ice, and passed 40 times in a dounce homogenizer to recover nuclei. For mitotic cells, the homogenization step was omitted. Mitotic and interphase cells were then treated in parallel to sonicate the chromatin in 300μl of TSE150 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl pH8, 150mM NaCl; freshly supplemented with 1× PIC) using 1.5ml tubes (Diagenode) and a Bioruptor Pico (Diagenode; 7 cycles divided into 30 s ON–30 s OFF sub-cycles at maximum power, in circulating ice-cold water). After centrifugation (30min, full speed, 4 °C), the supernatant was pre-cleared for 2h with 50μl of protein G Sepharose beads (P3296-5 ML Sigma) 50% slurry, previously blocked with BSA (500 μg/ml; 5931665103 Roche) and yeast tRNA (1 μg/ml; AM7119 Invitrogen). 20μl were set apart (input) before over-night immunoprecipitation at 4°C on a rotating wheel with 4µl of anti-CTCF (Active Motif 61311) or 4µl of anti-SMC1 (Bethyl Laboratories A300-055A) antibodies in 500μl of TSE150. Protein G beads (25μL 50% slurry) were added for 4 h rotating on-wheel at 4 °C. Beads were pelleted and washed for 15min rotating on-wheel at 4 °C with 1ml of the following buffers: 3 washes with TSE150, 1 wash with TSE500 (as TSE150 but 500 mM NaCl), 1 wash with Washing buffer (10mM Tris-HCl pH8, 0.25M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and 2 washes with TE (10mM Tris-HCl pH8, 1mM EDTA). Elution was performed in 100μl of elution buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8) for 15min at 65 °C after vigorous vortexing. Eluates were collected after centrifugation and beads rinsed in 150μl of TE-SDS1%. After centrifugation, the supernatant was pooled with the corresponding first eluate. For both immunoprecipitated and input chromatin, the crosslinking was reversed overnight at 65 °C, followed by proteinase K treatment, phenol/chloroform extraction and ethanol precipitation. H3 ChIP-seq was performed on MNase-digested chromatin using 2.5x106 cells fixed with formaldehyde as described above. Fixed cells were resuspended in 500µl of MNase buffer (50 mM Tris-HCl pH8, 1 mM CaCl2, 0.2% Triton X-100) supplemented with protease inhibitor cocktail (PIC; 04 693 116 001 Roche). Cells were pre-incubated for 10min at 37°C with 16U of MNase (Expressed in KUntiz, 1 Kunitz is equivalent to 10 gel units, NEB M0247S) added to the reaction. Cells were incubated for further 10min at 37°C, inverting the tubes occasionally. The reaction was stopped on ice by adding 500μl of 2×STOP buffer (2% Triton X-100, 0.2% SDS, 300mM NaCl, 10mM EDTA). Tubes were left rotating overnight on a wheel to allow diffusion of the digested fragments. The cell suspension was spun down and the supernatant stored at -80°C. Subsequently, 50µl of chromatin were brought to a final volume of 500µl with TSE150 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl pH8, 150mM NaCl), freshly supplemented with protease inhibitor cocktail (PIC-Roche, 04 693 116 001), and ChIP was performed as described above using 5µg of anti-Histone H3 rabbit polyclonal (Abcam; ab1791).

treatment_protocol: To obtain mitotic ES cells (>95% purity as assessed by DAPI staining and microscopy), we used a nocodazole shake-off approach. To deplete CTCF-aid in interphase, cells were treated with 0.5mM auxin (IAA Sigma, I5148) for 2h; to deplete CTCF-aid in mitosis, the cells were first treated with nocodazole for 4h and then with nocodazole and IAA for 2h, after which they were harvested by shake-off. C2C12 cells were synchronised like ES cells except that slightly longer nocodazole treatment (7h) was required to improve the yield. NIH3T3 cells were first synchronised with a double thymidine block, followed by release and nocodazole treatment; first, 1.5x106 cells were seeded in 150mm dishes and grown with 2mM thymidine for 18h to enrich in cells arrested at the G1/S transition. After two washes with PBS, they were released for 8h in regular medium before being arrested again for 17h with 2mM Thymidine. After the double thymidine block the cells were washed twice with PBS and released in regular medium for 7h. Finally, cells were incubated with nocodazole for 6h and mitotic cells isolated by gentle tapping of the dishes against an immobilised surface.

tag: cell type

value: embryonic stem cell

tag: cell subtype

tag: cell cycle

value: I

tag: treatment


title: RNA-Seq Data from russet fruit skin 3

city: Hangzhou

first: Yuezhi

last: Wang

state: Zhejiang

address: Shiqiao Road No.139

country: China

institute: Zhejiang Academy of Agricultral Sciences

library_source: transcriptomic

data_processing:
The data quality control was performed by removing adapters and discarding poor quality reads from the raw data.
Alignment of the selected reads with the reference genome of Chinese white pear (Pyrus × bretschneideri) deposited in NCBI database was carried out by Hisat2 v2.0.4
Transcripts were assembled and annotated from the read alignment results by Cufflinks v2.1.1 with the method based on the reference annotation.
The gene expression levels was quantified by FPKM method. The DESeq R package (1.18.0) was employed for gene differential expression analysis.
Benjamini and Hochberg’s approach False Discovery Rate was used for multiple test correction.
Genome_build: Chinese white pear genome as the reference
Supplementary_files_format_and_content: tab delimilted file

organism: Pyrus pyrifolia

source_name: fruit skin

growth_protocol: Open growth condition

extract_protocol:
in liquid nitrogen
NEB Next® Ultra™ RNA Library Prep Kit (NEB, USA)

treatment_protocol: Healthy plant

tag: cultivar

value: Niitaka

tag: time

value: 80 DAA

tag: phenotype

value: russet

tag: tissue

value: fruit skin


title: P640_20% oxygen cultured

city: Vancouver

first: Alexander

middle: G

last: Beristain

state: BC

address: 950 West 28th Ave

department: Obstetrics & Gynecology

country: Canada

institute: The University of British Columbia

description: Gene expression from matrigel embedded extravillous and column cells

hyb_protocol: Standard affymetrix hybridization protocol

scan_protocol: Standard affymetrix scanning protocol

data_processing: The Oligo package for Bioconductor was used to read raw array data into the RStudio software and convert Affymetrix CEL files into an expression matrix of intensity values. Data pre-processing included background corrrection and normalization through a Robust Multichip Average (RMA) methodology in the Oligo package. This strategy allows for background subtraction, quantile normalization and summarization via median-polish. We also conducted soft intensity-based probe filtering using the Limma package. A total of 8,352 low intensity probes, 732 duplicate probes and 4,703 non-annotated probes were filtered out to generate the final clean dataset of 13,402 probes total.

label: biotin

organism: Homo sapiens

source_name: 5.1 week human placental explant cultured in 20% oxygen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip Whole Transcript (WT) Expression Arrays Protocol

growth_protocol: 5-8 week placental villi were microdisected from whole placenta and embedded in Matrigel matrix. Explants were cultured in DMEM F12 1:1 + penicillin-streptomycin + antibiotic-antimycotic

extract_protocol: RNA was isolated from extravillous and column cells using a protocol that combines Trixol LS + Qiagen clean-up columns + DNAse treatment to remove any contaminant gDNA. Quality control was performed using Agilent Bioanalyzer.

treatment_protocol: All explants were established in 5% oxygen for 24 hours and then subjected to another 48 hours of culture in either 1%, 5% or 20% oxygen.

value: Placental explant

tag: condition

value: 20% oxygen


title: RNA-Seq Data from russet fruit skin 1


title: MNaseH3_CTCFAID_M_plusIAA_1

value: M


title: FF91

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Gene-level signal were derived from CEL files using RMA algorithm implemented in oligo Bioconductor package. Batch effects were corrected using ComBat.

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with  miRNeasy FFPE kit (Qiagen) in accordance with the manufacture's protocol.

tag: gender

tag: age

tag: histology

tag: tissue source


title: MNaseH3_CTCFAID_M_minusIAA_1

value: minusIAA


title: RNA-Seq Data from russet fruit skin 2


title: MNaseH3_CTCFAID_I_plusIAA_1


title: P640_5% oxygen cultured

source_name: 5.1 week human placental explant cultured in 5% oxygen

value: 5% oxygen


title: MNaseH3_CTCFAID_M_minusIAA_2


title: E65

status: Public on Nov 04 2019

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description:
The cashmere goat, which produces cashmere wool, is a breed of Capra hircus.
small RNA
expressed_miRNA_TPM.txt

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:TGGAATTCTCGGGTGCCAAGG;end2:GATCGTCGGACTGTAGAACTCTGAAC) trimmed with fastx_clipper
discovering novel miRNAs using miRDeep2,then predicting miRNA target gene using miRanda
mapped using bowtie -v 1
detecting different expression miRNA (TPM value) using Fisher test
Genome_build: Capra hircus CHIR_1.0
Supplementary_files_format_and_content: tab-delimited text file includes miRNA TPM values for each Sample.

organism: Capra hircus

source_name: E65, embryonic skin sample

extract_protocol:
For small RNA-seq, the three skin samples at each developmental stage were mixed together, total RNA was extracted from the mixture. 3μg of each RNA sample was used for small RNA cDNA library preparation with Balancer NGS Library Preparation Kit for small/microRNA (GnomeGen, San Diego, CA, USA) based on manufacturer’s instruction. Briefly, RNAs were ligated to 3’ and 5’ adaptor sequentially, reverse transcribed to cDNA and PCR amplified. Whole library was applied to 10% native PAGE gel electrophoresis and bands corresponding to miRNA insertion were cut and eluted. After ethanol precipitation and washing, the purified small RNA libraries were quantified with Qubit Fluorometer (Invitrogen, Carlsbad, CA, USA), used for cluster generation and applied to Illumina GAIIx (Illumina, San Diego, CA, USA) 73 nt single-end sequencing and Illumina NextSeq 500 151 nt pair-end sequencing according to the manufacturer’s instructions. The small RNA libraries sequencing was perfomed in ABLife, Inc. (Wuhan, China).
Total RNA was extracted by using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and RQ1 DNase (Promega, Madison, WI, USA) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpec Plus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis.

value: skin

tag: developmental stage

value: embryo


title: P638_20% oxygen cultured

source_name: 6.3 week human placental explant cultured in 20% oxygen


title: P640_1% oxygen cultured

source_name: 5.1 week human placental explant cultured in 1% oxygen

value: 1% oxygen


title: E45

source_name: E45, embryonic skin sample


title: E65-3

description:
The cashmere goat, which produces cashmere wool, is a breed of Capra hircus.
expressed_gene_RPKM.txt

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (GATCGGAAGAGC) trimmed with fastx_clipper
mapped using tophat2 --microexon-search --no-coverage-search --b2-N 1
detecting different expression gene using edgeR
Genome_build: Capra hircus CHIR_1.0
Supplementary_files_format_and_content: tab-delimited text file includes gene RPKM values for each Sample. FASTA file (cds.fa) compatible with RPKM table.

extract_protocol:
For RNA-seq, total RNA was extracted from each embryo, 10 mg of total RNA was used for RNA sequencing (RNA-seq) library preparation. Polyadenylated mRNAs were purified and concentrated with Magnetic Beads Oligo (dT) (Invitrogen, Carlsbad, CA, USA) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95oC followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and applied to Illumine NextSeq 500 system 151 nt pair-end sequencing by ABlife, Inc. (Wuhan, China).
Total RNA was extracted by using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and RQ1 DNase (Promega, Madison, WI, USA) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpec Plus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis.


title: P638_5% oxygen cultured

source_name: 6.3 week human placental explant cultured in 5% oxygen


title: E65-1


title: MNaseH3_CTCFAID_I_minusIAA_1

value: CTCFAID

value: Histone H3 (Abcam ab1791)


title: P637_5% oxygen cultured

source_name: 7.1 week human placental explant cultured in 5% oxygen


title: MNaseH3_CTCFAID_I_minusIAA_2


title: E65-2


title: E55-2

source_name: E55, embryonic skin sample


title: E55-1


title: E55


title: E45-1


title: P638_1% oxygen cultured

source_name: 6.3 week human placental explant cultured in 1% oxygen


title: E55-3


title: TF_ML_D29: scRNAseq data from D29 mature organoids generated from the TF line (3 replicates)

city: Cambridge

first: Ayshwarya

last: Subramanian

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

country: USA

institute: Broad Institute

data_processing:
3' polyA RNA-seq
Cellranger toolkit (v2.1.1)
Genome_build: GrCh38
Supplementary_files_format_and_content: UMI count sparse matrix where rows are genes and columns are cells/barcodes, from the cellranger filtered gene matrix outputs

molecule: polyA RNA

source_name: iPSC cells

growth_protocol: Takasato et al., 2016

extract_protocol:
3' polyA RNA seq
10X Genomics Chromium Prep

value: iPSC cells

tag: day

tag: donor/line

value: Thermofisher (ThF)


title: TF_ML_D7: scRNAseq data from D7 organoids generated from the TF line (3 replicates)


title: AS_ML_D15: scRNAseq data from D15 organoids generated from the AS line (3 replicates X 2 experiments)

value: Alstem (AS)


title: AS_ML_D7: scRNAseq data from D7 organoids generated from the AS line (3 replicates)


title: TF_ML_D32: scRNAseq data from D32 mature organoids generated from the TF line (3 replicates)


title: TF_ML_D0: scRNAseq data from D0/iPSC stage

description: scRNAseq data from D0/iPSC stage


title: AS_ML_D29: scRNAseq data from D29 mature organoids generated from the AS line (3 replicates)


title: AS_ML_D0: scRNAseq data from D0/iPSC stage

description: scRNAseq data from D0/iPSC stage


title: whole blood-HIE-rep3

city: Shanghai

first: xiaohua

last: dong

address: 1111 XianXia Road

institute: Tongren Hospital, Shanghai Jiao Tong University School of Medicine,

description: lncRNA expression in HIE neonatal human blood

hyb_protocol: After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)
Raw data were normalized by Quantile algorithm, limma packages in R

source_name: Peripheral Blood

label_protocol: 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted and purified using PAXgeneTM  Blood RNA Kit (Cat#762174, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: disease state

value: neonatal HIE

value: Peripheral Blood


title: E45-3


title: E45-2


title: P637_20% oxygen cultured

source_name: 7.1 week human placental explant cultured in 20% oxygen

value: 20% oxygenn


title: whole blood-HIE-rep2


title: whole blood-HIE-rep1


title: whole blood-control-rep3

description: lncRNA expression in non-HIE neonatal human blood

value: control


title: whole blood-control-rep2


title: TF_ML_D15: scRNAseq data from D15 organoids generated from the TF line (3 replicates X 2 experiments)


title: EG006_IA_mADPs_RNASeq_1_1847_6

city: Kansas City

first: Elin

last: Grundberg

state: Missouri

address: 2401 Gillham Road

institute: CHILDREN'S MERCY HOSP (KANSAS CITY, MO)

description: HI.1847.006.Index_6.EG006_IA_mADPs_RNASeq_1

data_processing:
Raw reads were trimmed for quality (phred33 ≥30) and length (n≥32), and Illumina adapters were clipped off using Trimmomatic v. 0.35
Filtered reads were then aligned to the GRCh38 human reference using STAR v. 2.5.3a
Raw read counts of genes were obtained using htseq-count v.0.6.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited file containing RPKM values of each sample

source_name: Adipocytes from adipose tissue

extract_protocol:
Adipose tissue was digested with collagenase according to a modification of the Robdell method (Tchernof et al., 2006). Briefly, adipose tissue samples were digested with collagenase type 1 in Krebs-Ringer-Henseleit (KRH) buffer for 45 minutes at 37°C. Cell suspensions containing mature adipocytes and the stromal-vascular fraction (SVF) were then filtered with a nylon mesh and washed 3 times with KRH buffer. The nature of the buoyancy adipocytes allows them to float to the surface. Mature adipocytes were discarded and the remaining solution containing the SVF was centrifuged 1500 rpm for 5 minutes. The pellet was washed with pre-adipocyte growth medium (PGM) (DMEM-F12 supplemented with 10% calf serum, 1% penicillin-streptomycin, 17µM pantothenic acid, 33µM biotin, 100µM ascorbic acid and 2,5 µm/ml amphoB) followed by a second centrifugation. Cells were cryopreserved using freezing medium (PGM supplemented with 40% FBS and 10% DMSO). The medium was added to the pellet and was frozen with a temperature gradient (-1 °C/ minutes) and store at -80°C until analysis.
0.5 to 3 million cells were re-suspended in 500 uL TRIzol Reagent and total RNA was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA library preparations were carried out on 500 ng of RNA with RNA integrity number (RIN)>7 using the Illumina TruSeq Stranded Total RNA Sample preparation kit, according to manufacturer's protocol. Final libraries were analyzed on a Bioanalyzer and sequenced on the Illumina HiSeq

value: Adipocytes from visceral adipose tissue


title: EG005_IA_mADPs_RNASeq_1_1847_6

description: HI.1847.006.Index_19.EG005_IA_mADPs_RNASeq_1


title: EG008_IA_mADPs_RNASeq_1_1847_7

description: HI.1847.007.Index_7.EG008_IA_mADPs_RNASeq_1


title: P637_1% oxygen cultured

source_name: 7.1 week human placental explant cultured in 1% oxygen

value: Placental explant


title: EG007_SC_mADPs_RNASeq_1_1847_7

description: HI.1847.007.Index_2.EG007_SC_mADPs_RNASeq_1

value: Adipocytes from subcutaneous adipose tissue


title: EG006_SC_mADPs_RNASeq_1_1847_6

description: HI.1847.006.Index_5.EG006_SC_mADPs_RNASeq_1


title: EG008_SC_mADPs_RNASeq_1_1847_7

description: HI.1847.007.Index_4.EG008_SC_mADPs_RNASeq_1


title: EG006_SC_mADPs_RNASeq_1_2666_3

description: HI.2666.003.Index_5.EG006_SC_mADPs_RNASeq_1


title: EG004_SC_mADPs_RNASeq_1_1847_6

description: HI.1847.006.Index_12.EG004_SC_mADPs_RNASeq_1


title: EG007_IA_Stroma_RNASeq_1_2665_8

description: HI.2665.008.Index_4.EG007_IA_Stroma_RNASeq_1

source_name: SVF from adipose tissue

value: SVF from visceral adipose tissue


title: EG008_IA_Stroma_RNASeq_1_2665_8

description: HI.2665.008.Index_16.EG008_IA_Stroma_RNASeq_1


title: EG005_IA_Stroma_RNASeq_1_2665_7

description: HI.2665.007.Index_5.EG005_IA_Stroma_RNASeq_1


title: EG006_IA_Stroma_RNASeq_1_2665_7

description: HI.2665.007.Index_15.EG006_IA_Stroma_RNASeq_1


title: EG007_SC_Stroma_RNASeq_1_2665_8

description: HI.2665.008.Index_2.EG007_SC_Stroma_RNASeq_1

value: SVF from subcutaneous adipose tissue


title: EG004_IA_Stroma_RNASeq_1_2665_6

description: HI.2665.006.Index_7.EG004_IA_Stroma_RNASeq_1


title: EG008_SC_Stroma_RNASeq_1_2665_8

description: HI.2665.008.Index_7.EG008_SC_Stroma_RNASeq_1


title: EG005_SC_Stroma_RNASeq_1_2665_6

description: HI.2665.006.Index_19.EG005_SC_Stroma_RNASeq_1


title: AT-030_IA_RNA_1_2364_3

source_name: Adipose Tissue

value: Visceral Adipose Tissue


title: AT-039_IA_RNA_1_2364_3


title: AT-021_IA_RNA_1_2364_2


title: AT-024_IA_RNA_1_2364_3


title: AT-018_IA_RNA_1_2364_2


title: EG006_IA_mADPs_RNASeq_1_2666_3

description: HI.2666.003.Index_6.EG006_IA_mADPs_RNASeq_1


title: EG004_SC_Stroma_RNASeq_1_2665_6

description: HI.2665.006.Index_2.EG004_SC_Stroma_RNASeq_1


title: AT-030_SC_RNA_1_2630_8

value: Subcutaneous Adipose Tissue


title: AT-024_SC_RNA_1_2630_8


title: AT-021_SC_RNA_1_2630_6


title: AT-045_SC_RNA_1_2630_8


title: AT-039_SC_RNA_1_2630_8


title: AT-010_IA_RNA_1_2364_1


title: AT-012_IA_RNA_1_2364_2


title: AT-010_SC_RNA_1_2630_5


title: AT-012_SC_RNA_1_2630_6


title: AT-008_SC_RNA_1_2630_5


title: AT-008_IA_RNA_1_2364_1


title: AT-018_SC_RNA_1_2630_6


title: EG006_SC_Stoma_RNASeq_1_2665_7

description: HI.2665.007.Index_6.EG006_SC_Stoma_RNASeq_1


title: AT-045_IA_RNA_1_2364_3


title: AT-004_SC_RNA_1_2630_5


title: whole blood-control-rep1

description: lncRNA expression in non-HIE neonatal human blood


title: AT-004_IA_RNA_1_2364_1


title: S. cerevisiae_BY4741_SO2 60min_ biological rep3

city: Vila Real

first: Ana

last: Mendes-Ferreira

address: Quinta de Prados

country: Portugal

institute: Universidade de Trás-os-Montes e Alto Douro

description: Gene expression data from cells incubated for 60 min  in the presence of sulphur dioxide

hyb_protocol: 5 µg of fragmented aRNA was used in a 100-µl hybridization cocktail containing added hybridization controls. 80 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0003; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: MAS 5.0

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae_BY4741_SO2 60min

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Yeast Genome 2.0 Arrays, according to the manufacturer's GeneChip 3' IVT Express kit user manual. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction (GeneChip 3' IVT Express Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3' IVT Express Kit; Affymetrix). Size distribution of the aRNA and fragmented aRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

extract_protocol: Total RNA isolation was performed using the hot-phenol method (Koher & Domdey, 1991, Methods in Enzimology 194:398-405).

treatment_protocol: Cells of S. cerevisiae BY4741 and of the mutant BY4741_∆com2 were cultivated in MMB growth medium (at pH 3.5) in the absence (Control) or presence (Treatment) of sulphur dioxide.

tag: strain

value: BY4741 (MATa, his3-delta-1, leu2-delta-0, met15-delta-0, ura3-delta-0)


title: S. cerevisiae_BY4741_SO2 60min_ biological rep1

growth_protocol: Cells of S. cerevisiae BY4741 and of the mutant BY4741_∆com2 were cultivated in MMB growth medium (at pH 3.5)


title: S. cerevisiae_BY4741_SO2 60min_ biological rep2


title: S. cerevisiae_BY4741_Control 60min_ biological rep2

description: Gene expression data from cells incubated for 60 min  in the absence of sulphur dioxide

source_name: S. cerevisiae_BY4741_Control 60min


title: S. cerevisiae_BY4741_Control 60min_ biological rep3


title: S. cerevisiae_∆com2_Control 60min_ biological rep1

description: Gene expression data from cells incubated for 60 min in the absence of sulphur dioxide

source_name: S. cerevisiae_delta-com2_Control 60min


title: S. cerevisiae_∆com2_SO2 60min_ biological rep1

source_name: S. cerevisiae_delta-com2_SO2 60min


title: S. cerevisiae_∆com2_SO2 60min_ biological rep2


title: S. cerevisiae_∆com2_Control 60min_ biological rep3


title: S. cerevisiae_BY4741_Control 60min_ biological rep1


title: S. cerevisiae_∆com2_SO2 60min_ biological rep3


title: U87 MG human glioblastoma cell line treated with Si306 and 10 Gy of proton dose - replicate1

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

institute: IBSBC CNR

description: Biological replicate 1 of 6

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to an established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2505B (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Agilent Data Processing Protocol Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. FeatureExtractor_Version: 9.5.3.1. Protocol_Name: GE2-v5_95_Feb07.

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. Untreated U87 glioblastoma cells were used as control of U87 samples treated with 2 and 10 Gy. U87 2Gy and U8710 Gy were used as controls of U87 Si306+2Gy and U87 Si306+10Gy combined treatments, respectively.  Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA from control samples was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: U87 MG glioblastoma cell lines were collected after 24 hours post proton treatments with 2 and 10 Gy and Si306 and proton combined treatments.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: cell line

value: U87 MG

tag: harvest time post treatment

value: 24 hours

tag: cell type

value: U87 MG human glioblastoma cell line

source_name: U87 glioblastoma cell line exposed to 10 Gy of proton beam

value: U87 MG glioblastoma cell line

value: exposed to 10 Gy of proton beam


title: U87 MG human glioblastoma cell line treated with Si306 and 2 Gy of proton dose - replicate4

description: Biological replicate 4 of 6

tag: treatment

source_name: U87 glioblastoma cell line exposed to 2 Gy of proton beam

value: exposed to 2 Gy of proton beam


title: S. cerevisiae_∆com2_Control 60min_ biological rep2


title: U87 MG human glioblastoma cell line treated with Si306 and 2 Gy of proton dose - replicate5

description: Biological replicate 5 of 6


title: U87 MG human glioblastoma cell line treated with Si306 and 10 Gy of proton dose - replicate2

description: Biological replicate 2 of 6


title: U87 MG human glioblastoma cell line treated with Si306 and 2 Gy of proton dose - replicate6

description: Biological replicate 6 of 6


title: U87 MG human glioblastoma cell line treated with 10 Gy of proton dose - replicate6

description: Biological replicate 6 of 6

value: treated with 10 Gy of proton dose

source_name: U87 glioblastoma untreated cell line

value: untreated


title: U87 MG human glioblastoma cell line treated with Si306 and 10 Gy of proton dose - replicate3

description: Biological replicate 3 of 6


title: U87 MG human glioblastoma cell line treated with Si306 and 10 Gy of proton dose - replicate6

description: Biological replicate 6 of 6


title: U87 MG human glioblastoma cell line treated with 10 Gy of proton dose - replicate4

description: Biological replicate 4 of 6


title: U87 MG human glioblastoma cell line treated with Si306 and 2 Gy of proton dose - replicate1

description: Biological replicate 1 of 6


title: U87 MG human glioblastoma cell line treated with Si306 and 10 Gy of proton dose - replicate4

description: Biological replicate 4 of 6


title: U87 MG human glioblastoma cell line treated with Si306 and 2 Gy of proton dose - replicate3

description: Biological replicate 3 of 6


title: U87 MG human glioblastoma cell line treated with 2 Gy of proton dose - replicate6

description: Biological replicate 6 of 6

value: treated with 2 Gy of proton dose


title: U87 MG human glioblastoma cell line treated with 10 Gy of proton dose - replicate2

description: Biological replicate 2 of 6


title: U87 MG human glioblastoma cell line treated with Si306 and 2 Gy of proton dose - replicate2

description: Biological replicate 2 of 6


title: U87 MG human glioblastoma cell line treated with 2 Gy of proton dose - replicate4

description: Biological replicate 4 of 6


title: U87 MG human glioblastoma cell line treated with 10 Gy of proton dose - replicate3

description: Biological replicate 3 of 6


title: U87 MG human glioblastoma cell line treated with Si306 and 10 Gy of proton dose - replicate5

description: Biological replicate 5 of 6


title: U87 MG human glioblastoma cell line treated with 10 Gy of proton dose - replicate5

description: Biological replicate 5 of 6


title: U87 MG human glioblastoma cell line treated with 2 Gy of proton dose - replicate5

description: Biological replicate 5 of 6


title: U87 MG human glioblastoma cell line treated with 2 Gy of proton dose - replicate3

description: Biological replicate 3 of 6


title: U87 MG human glioblastoma cell line treated with 2 Gy of proton dose - replicate2

description: Biological replicate 2 of 6


title: U87 MG human glioblastoma cell line treated with 10 Gy of proton dose - replicate1

description: Biological replicate 1 of 6


title: U87 MG human glioblastoma cell line treated with 2 Gy of proton dose - replicate1

description: Biological replicate 1 of 6


title: HepG2, miR-183 and Poly(I:C) treated

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: ON

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

institute: University of Ottawa

description: Gene expression data from HepG2 transfected with miR-183 mimic and stimulated with Poly(I:C)

hyb_protocol: cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Affymetric Expression Console using default analysis settings

label: Biotin Allonamide Triphosphate

source_name: HepG2 Hepatoma cells

label_protocol: Biotinylated cRNA were prepared using the Affimetrix GeneChip™ WT PLUS Reagent Kit with Biotin Allonamide Triphosphate from 5.5 ug total RNA

growth_protocol: Human hepatoma (HepG2) cells  were grown at 37°C in DMEM (Gibco, Life Technologies) with 10% FBS (Wisent)

extract_protocol: RNA isolation was performed using the RNeasy (Qiagen) isolation kit as per manufacturer’s protocol

treatment_protocol: on day one, cells were seeded at 5x10^5 cells per well in a 6-well plate and reverse transfected with mimics at 50nM. 48h post transfection, cells were stimulated with Poly(I:C) for 24h (500ng/mL).

tag: transfected mimics


title: SN14

city: Cincinnati

first: Douglas

last: Millay

state: OH

address: 240 Albert Sabin Way  MLC 7020

institute: Cincinnati Children's Hospital Medical Center

description: 3 weeks post-NBPI

data_processing:
FASTQ sequence reads were pseudoaligned using Kallisto Software (version 0.42.1) against Mouse transcriptome EnsMart72/mm10
Expression input analyzed by AltAnalyze (version 2.1.0)
Expression output as transcripts per million (TPM) filtered by adjP value and 2-fold change in gene expression
Genome_build: Mouse EnsMart72/mm10
Supplementary_files_format_and_content: Txt; xlsx

source_name: Biceps muscle, contralateral control, mouse 3 (JF9)

growth_protocol: Mice housed under standard conditions (source: Charles River)

extract_protocol:
Total RNA was extracted from biceps muscles using the ReliaPrep RNA Tissue Miniprep System (Promega), RNA quality and yield determined using Agilent BioAnalyzer and submitted for RNA-Seq analysis.
RNA was amplified using the Ovation RNA-Seq system V2 (NuGEN), constructed into cDNA libraries using the Nextera XT DNA sample preparation kit (Illumina) and sequenced on the HiSeq 2500 system (Illumina, Paired-End 75bp Flow Cell) to a depth of at least 35-40 million reads

treatment_protocol: Unilateral neonatal brachial plexus injury by excision of C5-T1 at postnatal age day 5 with harvest of bilateral biceps muscles 3 weeks post-denervation by snap freezing

tag: group

value: Contralateral Control

value: Postnatal age day 26


title: SN12

description: 3 weeks post-NBPI

source_name: Biceps muscle, contralateral control, mouse 2 (JF6)


title: HepG2, con-miR mimic transfected and Poly(I:C) treated

description: Gene expression data from HepG2 transfected with control mimic and stimulated with Poly(I:C)

value: con-miR (50nM)


title: SN11

description: 3 weeks post-NBPI

source_name: Biceps muscle, denervated, mouse 2 (JF6)

value: Denervated


title: SN10

description: 3 weeks post-NBPI

source_name: Biceps muscle, contralateral control, mouse 1 (JF2)


title: SN9

description: 3 weeks post-NBPI

source_name: Biceps muscle, denervated, mouse 1 (JF2)


title: dcre1

city: Beijing

first: Jing

last: Sun

address: No. 1 West Beichen Road

department: IGDB

institute: Chinese Academy of Sciences

description: high-throughput profiling of transcriptome in wild type mouse

data_processing:
RNA-seq was performed using Illumina HiSeq2500  > 45 million 2 × 100 reads per sample was produced and alignment was performed using mouse genome database GRCm38 version 67. Only uniquely and properly mapped read pairs were used for further analysis. FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. Differentially expressed genes (DEGs) were identified using the DESeq (2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution. The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using multivariate analysis of transcript splicing (MATS).
Genome_build: GRCm38
Supplementary_files_format_and_content: bigWig(bw)

source_name: adult brain

growth_protocol: Mice were housed in the animal facility at Institute of Genetics and Developmental Biology (IGDB), Chinese Academy of Sciences, on a 12-h reverse light/dark cycle with lights on at 0800 hour. All procedures and husbandry were performed according to protocols approved by the Institutional Animal Care and Use Committee at IGDB. All mice in the study were backcrossed to the C57BL/6 background for at least six generations.

extract_protocol:
Add 600 μl Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μl miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min.  B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube.  C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase.  D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through.  E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube.  F. The 10 μl DNase I and 70 μl Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 min.  G. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube.  H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3.  I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the center of the filter. Leave it at the room temperature for 2 min. Spin for ~20–30 sec at maximum speed to recover the RNA. Collect the eluate (which contains the RNA) and store it at –70°C.
Purify and Fragment mRNA  a. Add 50 μl RNA Purification Beads to each well with 50 μl total RNA (4μg) and mix thoroughly.  b. Incubate at 65°C for 5 min, remove at 4°C, and then place at room temperature for 5 min.  c. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well.  d. Remove the magnetic stand, add 200 μl of Bead Washing Buffer in each well, and mix thoroughly.  e. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well.   f. Add 50 μl of Elution Buffer in each well and mix thoroughly.  g. Incubate at 80°C for 2 min, remove at 25°C, and then place at room temperature.  h. Add 50 μl of Beads Binding Buffer in each well and mix thoroughly. The mixture was placed at room temperature for 5 min.  i. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well.  j. Remove the magnetic stand, add 200 μl of Bead Washing Buffer in each well, and mix thoroughly.  k. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well.  l. Remove the magnetic stand, add 19.5 μl of Elute, Primer,Fragment Mix in each well and mix thoroughly.  m. Incubate at 94°C for 8 min, remove at 4°C, and then centrifuge.  2.2 Synthesize First Strand cDNA  a. Add 8 μl First Strand Synthesis Act D Mix and SuperScript II Reverse Transcriptase in each well and mix thoroughly.  b. The mixture was incubated in the following progress: 25°C for 10 min, 42°C for 15 min, 70°C for 15 min, hold at 4°C.  2.3 Synthesize Second Strand cDNA  a. Add 5 μl End Repair Control (2 μl End Repair Control + 98 μl Resuspension Buffer) in each well.  b. Add 20 μl Second Strand Marking Master Mix and mix thoroughly.   b. The mixture was incubated at 16°C for 60 min.  2.3.1 Purification  a. Add 90 μl mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min.  b. Place it on the magnetic stand at room temperature for 5 min.   c. Remove and discard all of the supernatant from each well.  d. Place the plate on the magnetic stand. Add 200 μl of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well.  e. Repeat the above progress: place the plate on the magnetic stand; add 200 μl of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well.  f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand.  g. Add 17.5 μl Resuspension Buffer and mix thoroughly.  h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min.  i. Transfer 15 μl the supernatant from each well into the new PCR plate.  2.4 Adenylate 3’Ends  a. Add 2.5 μl diluted A-Tailing Control (1 μl A-Tailing Control + 99 μl Resuspension Buffer) in each well.  b. Add 12.5 μl A-Tailing Mix and mix thoroughly.   c. The mixture was incubated in the following progress: 37°C for 30 min, 70°C for 5 min, hold at 4°C.  2.5 Ligate Adapters  a. Add 2.5 μl diluted Ligation Control (1 μl Ligation Control + 99 μl Resuspension Buffer) in each well.  b. Add 2.5 μl Ligation Mix.  c. Add 2.5 μl RNA Adapter Index and mix thoroughly.  d. The mixture was incubated at 30°C for 10 min.  e. Add 5 μl Stop Ligation Buffer in each well and mix thoroughly.  2.5.1 Purification  a. Add 42 μl mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min.  b. Place it on the magnetic stand at room temperature for 15 min.   c. Remove and discard 79.5 μl of the supernatant from each well.  d. Place the plate on the magnetic stand. Add 200 μl of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well.  e. Repeat the above progress: place the plate on the magnetic stand; add 200 μl of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well.  f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand.  g. Add 52.5 μl Resuspension Buffer and mix thoroughly.  h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min.  i. Transfer 50 μl the supernatant from each well into the new PCR plate.  j. Add 50 μl mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min.  k. Place it on the magnetic stand at room temperature for 15 min.   l. Remove and discard 95 μl of the supernatant from each well.  m. Place the plate on the magnetic stand. Add 200 μl of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well.  n. Repeat the above progress: place the plate on the magnetic stand; add 200 μl of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well.  o. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand.  p. Add 22.5 μl Resuspension Buffer and mix thoroughly.  q. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min.  r. Transfer 20 μl the supernatant from each well into the new PCR plate.  2.6 Enrich DNA Fragments  a. Add 5 μl PCR Primer Cocktail.  b. Add 25 μl PCR Master Mix and mix thoroughly.   c. The mixture was incubated in the following progress: 1 cycle 98°C for 30 sec; 15 cycles 98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec; 1 cycle 72°C for 5 min; hold at 10°C.  2.7.1 Purification  a. Add 50 μl mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min.  b. Place it on the magnetic s

treatment_protocol: No treatment

tag: strain background

tag: tissue

value: Neural Stem Cell

tag: genotype

value: WT

value: P56 adult


title: dcre3

tag: age


title: dcre2


title: HepG2, miR-182 and Poly(I:C) treated

description: Gene expression data from HepG2 transfected with miR-182 mimic and stimulated with Poly(I:C)


title: SN13

description: 3 weeks post-NBPI

source_name: Biceps muscle, denervated, mouse 3 (JF9)


title: Mouse 40

city: Nijmegen

first: Jeroen

last: de Baaij

address: Geert Grooteplein Zuid 28

department: Physiology

country: Netherlands

institute: Radboudumc

data_processing:
Sample quality control, library preparation and RNA-sequencing was executed by BaseClear B.V., Leiden, The Netherlands. Briefly, on total RNA samples polyadenylated RNA enrichment for mRNA and removal of rRNA was performed.
After fitting of adapter sequences on amplicons during cDNA synthesis and PCR amplification the samples were sequenced on an Illumina HiSeq 2500 platform (Illumina, USA), using single-end sequencing and 10 million reads per sample.
The raw data were first subjected to a quality check using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the results were manually inspected for bad samples. Based on the QC analysis, no samples were removed from the data set.
Counts of transcripts per sample, expressed as the absolute number of reads and as normalized values (transcripts per million) were generated by using Salmon.4 The reference transcriptome, including gene annotations and gene-ontology mappings was downloaded from the BioMart repository at Ensembl (C57BL_6NJ_v1 at www.ensembl.org).
Genome_build: C57BL_6NJ_v1, mm10
Supplementary_files_format_and_content: Salmon quantification file

source_name: Thoracic aorta

growth_protocol: Animals were housed under standard circumstances

extract_protocol:
RNA was isolated according to the manufacturers protocol of TRIzol (Invitrogen) and always kept on ice. RNA was not subjected to DNAse treatment prior to sequencing.
Library preparation was performed by BaseClear B.V. Leiden, the Netherlands

treatment_protocol: Animals were divided in groups receiving a minimal or high (respectively 0.05% w/w or a 0.48% w/w) magnesium diet from birth untill 8 weeks of age.

value: 8 weeks post natal

value: Klotho-/-

value: Aorta

tag: treatment diet

value: Minimal magnesium


title: Mouse 39

value: Wild-type


title: Pggt1b_KO [XDU915]

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

description: XDU915_582558_mogene2st.rma-gene-full-Signal

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: Pggt1b_KO_CD4SP thymocytes

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Thymus were isolated and sorted for CD4SP thymocytes.

extract_protocol: Total RNA samples were prepared according to the prototol of RNeasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from RNeasy Micro kit from Qiagen.

tag: genotype/variation

value: CD4SP thymocytes


title: cre2

description: high-throughput profiling of transcriptome in HuRf/f KO mouse

value: HuRf/f KO


title: Pggt1b_KO [XDU918]

description: XDU918_582561_mogene2st.rma-gene-full-Signal


title: cre1


title: WT [XDU914]

description: XDU914_582557_mogene2st.rma-gene-full-Signal

source_name: WT_CD4SP thymocytes


title: Pggt1b_KO [XDU912]

description: XDU912_582555_mogene2st.rma-gene-full-Signal


title: cre3


title: WT [XDU911]

description: XDU911_582554_mogene2st.rma-gene-full-Signal


title: HepG2, miR-96 mimic transfected and Poly(I:C) treated

description: Gene expression data from HepG2 transfected with miR-96 mimic and stimulated with Poly(I:C)


title: Mouse 38


title: WT [XDU917]

description: XDU917_582560_mogene2st.rma-gene-full-Signal


title: Mouse 37


title: Mouse 36


title: Pggt1b_KO [XDU916]

description: XDU916_582559_mogene2st.rma-gene-full-Signal


title: Mouse_LDLR_M_Liver_RNAseq_PolyA_Chow_rep3

city: La Jolla

first: Jason

middle: Samuel

last: Seidman

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

description:
RNA-Seq. Fastq files from sequencing experiments were mapped to the mouse mm10 genome using default parameters for STAR .Mapped data were analyzed with HOMER's "analyzeRepeats.pl" function with options -raw -condenseGenes and -count exons. Differential expression was performed using Homer's getDiffExpression.pl function, which uses DESeq2.
Chow_raw.txt
Chow_TPM.txt
Chow_diffOutput.txt

data_processing:
All data were aligned to the mm10 assembly of the mouse genome, and all subsequent data analysis was performed using HOMER, and detailed instructions for analysis can be found at http://homer.salk.edu/homer/ . Mapped data were analyzed with HOMER's "analyzeRepeats.pl" function with options -raw -condenseGenes and -count exons. Differential expression was performed using Homer's getDiffExpression.pl function, which uses DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: DiffOutput file contains DESeq2 output for comapring Ldlr-/- to E06-scFvLdlr-/- livers. Table include calclated fold changes and adjusted p-values, as well as rlog normalized expression vaues of each gene for each sample.

source_name: RNA of liver isolated from Ldlr-/- or E06-scFvLdlr-/- mice fed chow diet

extract_protocol:
Liver RNA from indicated mice was extracted using trizol method prior to library preparation.
PolyA RNA was first selected from total RNA using magnetic oligo(dT)25 Dynabeads (Life Technologies) and multiple washes with 2× DTBB buffer (1 M Tris·HCl, 8 M LiCl, 0.5 M EDTA, 1% lithium dodecyl sulfate, and 0.1% Triton X100). Poly A enriched mRNA was fragmented in 2x Superscript III first-strand buffer with 10mM DTT (Invitrogen), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 µL of fragmented mRNA, 0.5 µL of Random primer (Invitrogen), 0.5 µL of Oligo dT primer (Invitrogen), 0.5 µL of SUPERase-In (Ambion), 1 µL of dNTPs (10 mM) and 1 µL of DTT (10 mM) were heated at 50°C for three minutes. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100 mM), 0.1 µL Actinomycin D (2 µg/µL), 0.2 µL of 1% Tween-20 (Sigma) and 0.2 µL of Superscript III (Invitrogen) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads according to manufacturer’s instruction and eluted with 10 µL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL of Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL of RNAse H (5 U/µL), 1.05 µL of water, 1 µL of DNA polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C for 1 hour. The resulting dUTP-marked dsDNA was purified using 28 µL of Sera-Mag Speedbeads (Thermo Fisher Scientific), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 µL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen -80°C. The purified dsDNA (40 µL) underwent end repair by blunting, A-tailing and adapter ligation using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 9-14 cycles, size selected by gel extraction, quantified Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on a Hi-Seq 4000 (Illumina) using single-end 75bp reads.

value: Ldlr-/-

tag: diet

value: Chow


title: Mouse_LDLR_M_Liver_RNAseq_PolyA_Chow_rep2


title: Mouse_LDLR_M_Liver_RNAseq_PolyA_Chow_rep1


title: Mouse 30

value: High magnesium


title: Mouse 29


title: Mouse 31


title: Mouse 32


title: Mouse 25


title: Mouse 26


title: Mouse_E06Ldlr_M_Liver_RNAseq_PolyA_Chow_rep3


title: Mouse_E06Ldlr_M_Liver_RNAseq_PolyA_Chow_rep1


title: Mouse 20


title: Mouse_LDLR_M_Liver_RNAseq_PolyA_AMLN_rep1

description:
RNA-Seq. Fastq files from sequencing experiments were mapped to the mouse mm10 genome using default parameters for STAR .Mapped data were analyzed with HOMER's "analyzeRepeats.pl" function with options -raw -condenseGenes and -count exons. Differential expression was performed using Homer's getDiffExpression.pl function, which uses DESeq2.
AMLN_raw.txt
AMLN_TPM.txt
AMLN_diffOutput.txt

source_name: RNA of liver isolated from Ldlr-/- or E06-scFvLdlr-/- mice fed AMLN diet

value: AMLN


title: Mouse 23


title: Mouse_E06Ldlr_M_Liver_RNAseq_PolyA_Chow_rep2


title: shARID1A-2

first: Qingyu

last: Luo

address: Panjiayuannanli No.17#, Chaoyang District

department: State Key Laboratory of Molecular Oncology

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: Gene expression in shARI group

hyb_protocol: The labelled cRNAs were then hybridized onto the microarray.

scan_protocol: After the arrays were washed, they were scanned by an Agilent Microarray Scanner G2505C

data_processing: Feature Extraction Software (version 10.7.1.1, Agilent Technologies) was used to analyse the array images to obtain the raw data. GeneSpring (version 13.1, Agilent Technologies) was employed to complete the basic analysis of the raw data.

source_name: human esophagus cancer cell line

label_protocol: Total RNA was transcribed to double-stranded cDNA, synthesized into cRNA and labelled with cyanine-3-CTP.

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS

extract_protocol: Total RNA was isolated from cells using TRIzol reagent

treatment_protocol: Cells were transfected with either an ARID1A-targeting shRNA sequence or a non-targeting shRNA sequence then selected with puromycin

value: Human oesophageal squamous cell carcinoma


title: shARID1A-3

description: Gene expression in shARI group


title: Mouse_LDLR_M_Liver_RNAseq_PolyA_AMLN_rep2


title: Mouse 35


title: shControl-1

description: Gene expression in shCtrl group


title: shARID1A-1

description: Gene expression in shARI group


title: Mouse_E06Ldlr_M_Liver_RNAseq_PolyA_AMLN_rep2


title: Mouse_E06Ldlr_M_Liver_RNAseq_PolyA_AMLN_rep1


title: shControl-2

description: Gene expression in shCtrl group


title: WT [XDU913]

description: XDU913_582556_mogene2st.rma-gene-full-Signal


title: Mouse 13


title: Mouse 12


title: shControl-3

description: Gene expression in shCtrl group


title: Mouse_E06Ldlr_M_Liver_RNAseq_PolyA_AMLN_rep3


title: AGO2 IP FMR1 ko mouse

city: Urbana

first: Phillip

middle: James

last: Kenny

state: IL

address: 407 S. Goodwin

institute: University of Illinois, Urbana-Champaign

data_processing:
Library strategy: eCLIP-seq
Single-end (75nt) sequencing was performed on the HiSeq 4000 platform.
The first 10 nt of each read contains a unique molecular identifier (UMI) which was extracted from each read with UMI tools (version 5.2) and appended to the end of the read name.
Sequencing adapters were trimmed from the 3’ end of each read using Cutadapt (version 1.15).
Reads were then mapped to a database of mouse repeats using STAR (version 2.6.0c).  Reads that mapped to the repeats were removed. The remaining reads were mapped to the mouse genome (mm10) using STAR (version 2.6.0c).
PCR duplication removal was performed using UMI tools (version 5.2). CLIPper (version 1.4) was then used to identify clusters within the IP samples, and read density within clusters was compared against the size matched input sample using a custom perl script to identify peaks enriched in the CLIP sample versus the input sample.
Genome_build: Mouse Genome (mm10)

source_name: Brain

growth_protocol: Brains were flash frozen in LN2, packaged in dry ice, and sent to eClipse BioInnovations

extract_protocol:
Ago2 was immunoprecipitated using anti-AGO2 antibody EAG009 (eClipse BioInnovations).  Samples from each sample was normalized to input samples.
Sequencing adapters were trimmed from the 3’ end of each read using Cutadapt (version 1.15).  Reads were then mapped to a database of mouse repeats using STAR (version 2.6.0c).  Reads that mapped to the repeats were removed. The remaining reads were mapped to the mouse genome (mm10) using STAR (version 2.6.0c).  PCR duplication removal was performed using UMI tools (version 5.2). CLIPper (version 1.4) was then used to identify clusters within the IP samples, and read density within clusters was compared against the size matched input sample using a custom perl script to identify peaks enriched in the CLIP sample versus the input sample.

tag: background strain

value: whole brain

tag: developmental stage

value: FMR1 ko

tag: molecule subtype

value: Ago-associated mRNA


title: Mouse 11

tag: strain


title: Mouse adult, male 2, outer medulla

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

data_processing:
read length:  R1:27b, R2: 120b
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed; unused barcodes deleted
Reads were mapped using STAR 2.5.1b
Count tables were generated from the FASTQ files using the Cell Ranger software version 2.1 with default parameters.
Read 1 is the Cell Barcode + UMI and read 2 is the actual RNA sequence.  Read length:  R1:27b, R2: 120b.
bam file contains cell barcode for each read at CR:Z tag
Genome_build: mm10
Supplementary_files_format_and_content: gzip file Mouse_Adult_DGE.tar  containing matrix.mtx, genes.tsv, barcodes.tsv,  barcodes annotated with sample specific coding:  replicate F1,F2,M1 or M2; sex M or F; anatomic zone Z1, Z2 or Z3
load using Matrix and Seurat R packages with  "Read10X" function to yield unfiltered dgCMatrix  containing 27, 998 genes across 40, 712 cell profiles;  initialize Seurat object with filters min.cells =3, min.genes = 1000
gzip file Mouse_Adult_DGE_final.tar  filtered and processed matrix used for tSNE in Fig 1C. and Supplementary Table 1;  19,125 genes across 31,265 cells

source_name: kidney

extract_protocol:
10X Genomics Chromium v2 Single Cell 3’ protocol:  7-9,000 singlet live cells loaded/lane, cell capture, lysis and mRNA reverse transcription occurred in-droplets.  cDNA recovered from the emulsion was cleaned-up, amplified by PCR, checked for size and yield on a 4200 Tape station (Agilent), processed into barcoded Illumina ready sequencing libraries and again assayed for size and yield.
10X Genomics Chromium v2 Single Cell 3’ protocol:

tag: Stage

value: adult, 8-9 weeks

tag: Sex

value: male

value: kidney

tag: tissue zone

value: outer medulla


title: Mouse 10

value: 8 weeks post natal

value: Aorta


title: Mouse 16

value: Klotho-/-


title: Mouse adult, male 2, cortex

value: cortex


title: AGO2 Input Jax FMR1 ko mouse


title: Mouse adult, male 1, inner medulla

value: inner medulla


title: AGO2 IP Jax WT C57BL/6

value: wild type


title: Mouse 4

value: Wild-type

value: Minimal magnesium


title: Mouse adult, male 1, outer medulla


title: Mouse adult, male 1, cortex


title: Mouse adult, male 2, inner medulla


title: H3K27ac ChIP-seq [77_WT_Th0_IL6_H3K27ac]

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

description:
77_WT_Th0_IL6_H3K27ac
processed data file: 77_WT_Th0_IL6_H3K27ac.bedGraph.gz

data_processing:
fastq QC: fastqc
remove adapter: trim_galore v0.4.1
mapping: Bowtie1 (v1.1.2)
filter/remove duplicates: samtools v0.1.19
peak-calling: MACS2 v.2.1.0
normalization/tagcount/bedgraph: HOMER v4.9.0
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated using HOMER

source_name: CD4 T cell

growth_protocol: naïve CD4+ T cells isolated from spleen/lymph nodes were activated with 2 ug/ml anti-CD3 and 0.5 ug/ml anti-CD28

extract_protocol:
Cells (10 x 10e6) were cross-linked for 10 min with 1% formaldehyde, quenched with Glycine, and washed. Cell pellets were resuspended in lysis buffer, and homogenized. Nuclei were resuspended in RIPA buffer and sonicated to a size range of 200-500 bp using Bioruptor. Cells were pelleted, RIPA buffer was added to supernatant to 1 ml, and appropriate antibody coupled to Dynabeads M-280 Sheep anti-rabbit IgG  was added. The immunocomplexes were washed, supernatants were collected, incubated at 65oC overnight, and immunoprecipiated DNA were purified using MinElute columns (Qiagen)
[Antibodies] rabbit anti-BATF (Schraml et al., 2010), rabbit anti-CTCF (Active Motif, 61311), rabbit anti-Med12 (Bethyl, A300-774A),  rabbit anti-Ets1 (Santa Cruz, sc 350X), rabbit anti-IRF4 (Santa Cruz, sc-28696 X),  rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), and normal rabbit IgG (Millipore, 12-370)
Immunoprecipitated DNA was used to prepare library using NEBNext Ultra II DNA library prep kit and NEBNext Multiplex Oligos for Illumina (NEB). ChIP-seq libraries were sequenced with single-end 50 bp using Illumina HiSeq 2500.

treatment_protocol: treated with 20 ng/ml IL-6 or Th17 culture conditions (20 ng/ml IL-6; 5 ng/ml human TGFb; 10 ng/ml IL-1b, 10 ug/ml anti-IL-4, and 10 ug/ml anti-IFNg) for 24 h (D1) or 96 h (D4)

tag: strain/background

value: wild-type

value: spleen and lymph nodes

tag: cell type

value: Activated CD4+ T cells

tag: treatment

tag: chip antibody


title: HiC [10_Naive_BatfKO]

description:
10_Naive_BatfKO
processed data file: 6_Naive_BatfKO_PCA.PC1.bedGraph

data_processing:
fastq QC: fastqc
mapping: Hi-C Pro v2.7.0 pipeline
intra and inter-chromosomal interactions: HOMER v4.8
annotation: HOMER v4.8
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated using HOMER

source_name: CD4 T cells

extract_protocol:
activated CD4 T cells were harvested, washed with 1X PBS, cross-linked with 1% formaldehyde and nuclei were isolated. Cross-linked DNA was digested with HindIII and marked with biotin.
Biotinylated DNA was captured using magnetic streptavidin beads (Invitrogen), used for adaptor ligation reaction, and PCR amplification using NEBNext DNA Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primers Set, NEB). Hi-C libraries were sequenced with paired-end 50 bp using Illumina HiSeq 2500

treatment_protocol: treated with or without 20 ng/ml IL-6 96 h

value: BatfKO

tag: tissue

value: Naive CD4 T cells


title: H3K27me3 ChIP-seq [76_WT_Th0_IL6_H3K27me3]

description:
76_WT_Th0_IL6_H3K27me3
processed data file: 76_WT_Th0_IL6_H3K27me3.bedGraph.gz


title: Mouse adult, female 2, inner medulla

value: adult, 8-9 weeks

value: female


title: Mouse 1

tag: genotype


title: HiC [9_Naive_WT]

description:
9_Naive_WT
processed data file: 5_Naive_WT_PCA.PC1.bedGraph


title: Mouse adult, female 2, outer medulla

value: kidney


title: H3K4me3 ChIP-seq [75_WT_Th0_IL6_H3K4me3]

description:
75_WT_Th0_IL6_H3K4me3
processed data file: 75_WT_Th0_IL6_H3K4me3.bedGraph.gz


title: Mouse adult, female 2, cortex


title: Mouse 5

tag: age

value: High magnesium


title: HiC [8_BatfKO2_IL6]

description:
8_BatfKO2_IL6
processed data file: 4_BatfKO_IL6.PCA.PC1.bedGraph

data_processing:
fastq QC: fastqc
Mapping: Hi-C Pro v2.7.0 pipeline
Intra and inter-chromosomal interactions: HOMER v4.8
Annotation: HOMER v4.8
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedgraph files were generated using HOMER.

growth_protocol: Naïve CD4+ T cells isolated from spleen/lymph nodes were activated with 2 ug/ml anti-CD3 and 0.5 ug/ml anti-CD28.

extract_protocol:
Activated CD4 T cells were harvested, washed with 1X PBS, cross-linked with 1% formaldehyde and nuclei were isolated. Cross-linked DNA was digested with HindIII and marked with biotin.
Biotinylated DNA was captured using magnetic streptavidin beads (Invitrogen), used for adaptor ligation reaction, and PCR amplification using NEBNext DNA Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primers Set, NEB). Hi-C libraries were sequenced with paired-end 50 bp using Illumina HiSeq 2500.

treatment_protocol: Treated with or without 20 ng/ml IL-6 96 h.

tag: time point


title: HiC [7_BatfKO2]

description:
7_BatfKO2
processed data file: 3_BatfKO_PCA.PC1.bedGraph

tag: genotype/variation


title: Mouse adult, female 1, inner medulla


title: HiC [6_WT2_IL6]

description:
6_WT2_IL6
processed data file: 2_WT_IL6_PCA_PC1.bedGraph


title: Mouse adult, female 1, cortex


title: HiC [5_WT2]

description:
5_WT2
processed data file: 1_WT_PCA.PC1.bedGraph


title: Mouse adult, female 1, outer medulla

value: outer medulla


title: HY361-3

city: Chicago

first: Zachary

middle: Rockow

last: Chalmers

address: 303 E. Superior Ave

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19

growth_protocol: PC3 cells were routinely grown in RPMI media with 10% FBS and 1% Pen-strep.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy plus mini kit
A total amount of 50ng RNA used to prepared single-indexed strand-specific cDNA library using TruSeq RNA Access Library Prep Kit (Illumina).

treatment_protocol: Cells were plated, and next day 6 µM of 361 (in DMSO) was added to cells for 24h treatment. Control groups were treated with DMSO.

value: Prostate cancer cell line


title: HiC [4_BatfKO1_IL6]

description:
4_BatfKO1_IL6
processed data file: 4_BatfKO_IL6.PCA.PC1.bedGraph


title: HY361-1


title: ATAC-seq [29_D4_WT]

description:
29_D4_WT
processed data file: 29_D4_WT.bedGraph.gz

data_processing:
fastq QC: fastqc
Remove adapter: trim_galore v0.4.1
Mapping: Bowtie2 (v2.2.5)
Filter/remove duplicates: samtools v0.1.19/Picard v2.6.0
Peak-calling: MACS2 v.2.1.0
Normalization/tagcount/bedgraph: HOMER v4.9.0
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedgraph files were generated using HOMER.

extract_protocol:
Cells sorted from activated CD4 T cells, washed with 1X PBS, and nuclei were isolated. The transposition reaction was carried out using Nextera DNA Sample Preparation Kit.
Illumina

treatment_protocol: Treated with 20 ng/ml IL-6 or Th17 culture conditions (20 ng/ml IL-6; 5 ng/ml human TGFb; 10 ng/ml IL-1b, 10 ug/ml anti-IL-4, and 10 ug/ml anti-IFNg) for 24 h (D1) or 96 h (D4).


title: HYDMSO-2


title: HYDMSO-1


title: HiC [1_WT1]

description:
1_WT1
processed data file: 1_WT_PCA.PC1.bedGraph


title: ATAC-seq [30_D4_WT_IL6]

description:
30_D4_WT_IL6
processed data file: 30_D4_WT_IL6.bedGraph.gz


title: PC3_975_3

description:
processed data file:
PC3_Con_vs_975.htseq.edgeR.txt
PC3_975_3_S68

data_processing:
Alignment: Sequenced reads were aligned to the hg38 reference human genome using STAR (v. ).
Read Counting: Reads per gene were counted using htseq (v. ).
Differenial Expression Analysis: differentially expressed RNAs were identified using edgeR (v. ).
Genome_build: hg38
Supplementary_files_format_and_content: edgeR output including normalized read counts, and LFC

growth_protocol: P493-6 and PC3 cells were routinely grown in RPMI media with 10% FBS and 1% Pen-strep.

treatment_protocol: Cells were plated, and next day 8 µM of MYCi975 (in DMSO) was added in PC3 cells, and 6 µM of MYCi975 (in DMSO) or 0.1 µg/ml of tetracycline (in H2O) were added to P493-6 cells for 24h treatment. Control groups were treated with DMSO.

tag: cell line

value: 8 µM of MYCi975 (in DMSO)


title: HiC [2_WT1_IL6]

description:
2_WT1_IL6
processed data file: 2_WT_IL6_PCA_PC1.bedGraph


title: ATAC-seq [25_BATFKO1_Tfh]

description:
25_BATFKO1_Tfh
processed data file: 25_BATFKO_Tfh.bedGraph.gz

value: BATFKO

value: Tfh cells


title: PC3_Con_3

description:
processed data file:
PC3_Con_vs_975.htseq.edgeR.txt
PC3_Con_3_S62

value: none (control)


title: ATAC-seq [28_D1_WT_IL6]

description:
28_D1_WT_IL6
processed data file: 28_D1_WT_IL6.bedGraph.gz


title: ATAC-seq [24_WT2_Tfh]

description:
24_WT2_Tfh
processed data file: 23_WT_Tfh.bedGraph.gz


title: HYDMSO-3


title: ATAC-seq [23_WT1_Tfh]

description:
23_WT1_Tfh
processed data file: 23_WT_Tfh.bedGraph.gz


title: PC3_Con_1

description:
processed data file:
PC3_Con_vs_975.htseq.edgeR.txt
PC3_Con_1_S60


title: ATAC-seq [26_BATFKO2_Tfh]

description:
26_BATFKO2_Tfh
processed data file: 25_BATFKO_Tfh.bedGraph.gz


title: P493-6_tetra_3

description:
processed data file:
P493-6_Con_vs_Tetra.htseq.edgeR.txt
P493-6_tetra_3_S56

value: c-MYC overexpressing Burkitt lymphoma cell line

value: 0.1 µg/ml of tetracycline


title: HY361-2


title: PC3_Con_2

description:
processed data file:
PC3_Con_vs_975.htseq.edgeR.txt
PC3_Con_2_S61


title: ATAC-seq [22_D1_IRF4cKO_IL6]

description:
22_D1_IRF4cKO_IL6
processed data file: 18_D1_IRF4cKO_IL6.bedGraph.gz


title: HiC [3_BatfKO1]

description:
3_BatfKO1
processed data file: 3_BatfKO_PCA.PC1.bedGraph


title: Mouse 18

value: 8 weeks post natal

value: Klotho-/-

value: Aorta

tag: treatment diet

value: Minimal magnesium


title: ATAC-seq [21_D1_IRF4WT2_IL6]

description:
21_D1_IRF4WT2_IL6
processed data file: 17_D1_IRF4WT_IL6.bedGraph.gz

value: wild-type

value: spleen and lymph nodes

value: Activated CD4+ T cells


title: P493-6_tetra_2

description:
processed data file:
P493-6_Con_vs_Tetra.htseq.edgeR.txt
P493-6_tetra_2_S55


title: PC3_975_2

description:
processed data file:
PC3_Con_vs_975.htseq.edgeR.txt
PC3_975_2_S67


title: PC3_975_1

description:
processed data file:
PC3_Con_vs_975.htseq.edgeR.txt
PC3_975_1_S66


title: ATAC-seq [27_D1_WT]

description:
27_D1_WT
processed data file: 27_D1_WT.bedGraph.gz


title: P493-6_975_2

description:
processed data file:
P493-6_Con_vs_975.htseq.edgeR.txt
P493-6_975_2_S58

value: 6 µM of MYCi975 (in DMSO)


title: P493-6_tetra_1

description:
processed data file:
P493-6_Con_vs_Tetra.htseq.edgeR.txt
P493-6_tetra_1_S54


title: P493-6_975_1

description:
processed data file:
P493-6_Con_vs_975.htseq.edgeR.txt
P493-6_975_1_S57


title: ATAC-seq [18_D1_IRF4cKO1_IL6]

description:
18_D1_IRF4cKO1_IL6
processed data file: 18_D1_IRF4cKO_IL6.bedGraph.gz


title: ATAC-seq [20_D1_IRF4cKO2]

description:
20_D1_IRF4cKO2
processed data file: 16_D1_IRF4cKO.bedGraph.gz


title: ATAC-seq [19_D1_IRF4WT2]

description:
19_D1_IRF4WT2
processed data file: 15_D1_IRF4WT.bedGraph.gz


title: P493-6_975_3

description:
processed data file:
P493-6_Con_vs_975.htseq.edgeR.txt
P493-6_975_3_S59


title: P493-6_Con_2

description:
processed data file:
P493-6_Con_vs_975.htseq.edgeR.txt
P493-6_Con_vs_Tetra.htseq.edgeR.txt
P493-6_Con_vs_Tetra.htseq.edgeR.txt
P493-6_Con_2_S52


title: ATAC-seq [15_D1_IRF4WT1]

description:
15_D1_IRF4WT1
processed data file: 15_D1_IRF4WT.bedGraph.gz


title: ATAC-seq [14_D1_BATFKO2_IL6]

description:
14_D1_BATFKO2_IL6
processed data file: 9_D1_WT_IL6.bedGraph.gz


title: P493-6_Con_3

description:
processed data file:
P493-6_Con_vs_975.htseq.edgeR.txt
P493-6_Con_vs_Tetra.htseq.edgeR.txt
P493-6_Con_vs_Tetra.htseq.edgeR.txt
P493-6_Con_3_S53


title: ATAC-seq [11_D1_WT2]

description:
11_D1_WT2
processed data file: 7_D1_WT.bedGraph.gz


title: ATAC-seq [8_D1_BATFKO1]

description:
8_D1_BATFKO1
processed data file: 8_D1_BATFKO.bedGraph.gz


title: P493-6_Con_1

description:
processed data file:
P493-6_Con_vs_975.htseq.edgeR.txt
P493-6_Con_vs_Tetra.htseq.edgeR.txt
P493-6_Con_vs_Tetra.htseq.edgeR.txt
P493-6_Con_1_S51


title: ATAC-seq [10_D1BATFKO1_IL6]

description:
10_D1BATFKO1_IL6
processed data file: 10_D1_BATFKO_IL6.bedGraph.gz


title: ATAC-seq [7_D1_WT1]

description:
7_D1_WT1
processed data file: 7_D1_WT.bedGraph.gz


title: ATAC-seq [4_Naive_BATFKO2]

description:
4_Naive_BATFKO2
processed data file: 2_Naive_BATFKO.bedGraph.gz

value: Naive CD4+ T cells


title: ATAC-seq [6_BATFKO_Th17]

description:
6_BATFKO_Th17
processed data file: 6_BATFKO_Th17.bedGraph.gz


title: ATAC-seq [1_Naive_WT1]

description:
1_Naive_WT1
processed data file: 1_Naive_WT.bedGraph.gz


title: ATAC-seq [5_WT_Th17]

description:
5_WT_Th17
processed data file: 5_WT_Th17.bedGraph.gz


title: ATAC-seq [16_D1_IRF4cKO1]

description:
16_D1_IRF4cKO1
processed data file: 16_D1_IRF4cKO.bedGraph.gz


title: IRF4 ChIP-seq [74_D4_IRF4_WT2_IL6]

description:
74_D4_IRF4_WT2_IL6
processed data file: 65_D4_IRF4_WT_IL6.bedGraph.gz

data_processing:
fastq QC: fastqc
Remove adapter: trim_galore v0.4.1
Mapping: Bowtie1 (v1.1.2)
Filter/remove duplicates: samtools v0.1.19
Peak-calling: MACS2 v.2.1.0
Normalization/tagcount/bedgraph: HOMER v4.9.0
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedgraph files were generated using HOMER.

extract_protocol:
Cells (10 x 10e6) were cross-linked for 10 min with 1% formaldehyde, quenched with Glycine, and washed. Cell pellets were resuspended in lysis buffer, and homogenized. Nuclei were resuspended in RIPA buffer and sonicated to a size range of 200-500 bp using Bioruptor. Cells were pelleted, RIPA buffer was added to supernatant to 1 ml, and appropriate antibody coupled to Dynabeads M-280 Sheep anti-rabbit IgG was added. The immunocomplexes were washed, supernatants were collected, incubated at 65oC overnight, and immunoprecipitated DNA were purified using MinElute columns (Qiagen).
Antibodies: Rabbit anti-BATF (Schraml et al., 2010), rabbit anti-CTCF (Active Motif, 61311), rabbit anti-Med12 (Bethyl, A300-774A), rabbit anti-Ets1 (Santa Cruz, sc 350X), rabbit anti-IRF4 (Santa Cruz, sc-28696 X), and normal rabbit IgG (Millipore, 12-370).
Immunoprecipitated DNA was used to prepare library using NEBNext Ultra II DNA library prep kit and NEBNext Multiplex Oligos for Illumina (NEB). ChIP-seq libraries were sequenced with single-end 50 bp using Illumina HiSeq 2500.


title: ATAC-seq [9_D1_WT1_IL6]

description:
9_D1_WT1_IL6
processed data file: 9_D1_WT_IL6.bedGraph.gz


title: ATAC-seq [2_Naive_BATFKO1]

description:
2_Naive_BATFKO1
processed data file: 2_Naive_BATFKO.bedGraph.gz


title: ATAC-seq [17_D1_IRF4WT1_IL6]

description:
17_D1_IRF4WT1_IL6
processed data file: 17_D1_IRF4WT_IL6.bedGraph.gz


title: IRF4 ChIP-seq [73_D4_IRF4_WT2]

description:
73_D4_IRF4_WT2
processed data file: 64_D4_IRF4_WT.bedGraph.gz


title: ATAC-seq [13_D1_BATFKO2]

description:
13_D1_BATFKO2
processed data file: 8_D1_BATFKO.bedGraph.gz


title: IRF4 ChIP-seq [72_D4_IRF4_WT1_IL6]

description:
72_D4_IRF4_WT1_IL6
processed data file: 65_D4_IRF4_WT_IL6.bedGraph.gz


title: CTCF ChIP-seq [68_D1_CTCF_WT2]

description:
68_D1_CTCF_WT2
processed data file: 62_D1_CTCF_WT.bedGraph.gz

value: CTCF


title: CTCF ChIP-seq [70_D1_CTCF_WT2_IL6]

description:
70_D1_CTCF_WT2_IL6
processed data file: 63_D1_CTCF_WT_IL6.bedGraph.gz


title: CTCF ChIP-seq [69_D1_CTCF_WT1_IL6]

description:
69_D1_CTCF_WT1_IL6
processed data file: 63_D1_CTCF_WT_IL6.bedGraph.gz


title: IRF4 ChIP-seq [71_D4_IRF4_WT1]

description:
71_D4_IRF4_WT1
processed data file: 64_D4_IRF4_WT.bedGraph.gz


title: CTCF ChIP-seq [67_D1_CTCF_WT1]

description:
67_D1_CTCF_WT1
processed data file: 62_D1_CTCF_WT.bedGraph.gz


title: BATF ChIP-seq [66_BATF_BATFKO2]

description:
66_BATF_BATFKO2
processed data file: 61_BATF_BATFKO.bedGraph.gz

value: BATF


title: ATAC-seq [12_D1_WT2_IL6]

description:
12_D1_WT2_IL6
processed data file: 9_D1_WT_IL6.bedGraph.gz


title: Ets1 ChIP-seq [54_D4_Ets1_BATFKO2]

description:
54_D4_Ets1_BATFKO2
processed data file: 50_D4_Ets1_BATFKO.bedGraph.gz


title: Ets1 ChIP-seq [55_D4_Ets1_WT2_IL6]

description:
55_D4_Ets1_WT2_IL6
processed data file: 51_D4_Ets1_WT_IL6.bedGraph.gz


title: BATF ChIP-seq [65_BATF_BATFKO1]

description:
65_BATF_BATFKO1
processed data file: 61_BATF_BATFKO.bedGraph.gz


title: Mouse 9

value: Wild-type

value: High magnesium


title: Ets1 ChIP-seq [50_D4_Ets1_BATFKO1]

description:
50_D4_Ets1_BATFKO1
processed data file: 50_D4_Ets1_BATFKO.bedGraph.gz

value: BATFKO


title: ATAC-seq [3_Naive_WT2]

description:
3_Naive_WT2
processed data file: 1_Naive_WT.bedGraph.gz


title: AGO2 Input Jax WT C57BL/6

tag: background strain

value: whole brain

tag: developmental stage

value: wild type

value: Ago-associated mRNA


title: CTCF ChIP-seq [48_D4_CTCF_Ets1cKO2_IL6]

description:
48_D4_CTCF_Ets1cKO2_IL6
processed data file: 48_D4_CTCF_Ets1cKO_IL6.bedGraph.gz


title: Ets1 ChIP-seq [51_D4_Ets1_WT1_IL6]

description:
51_D4_Ets1_WT1_IL6
processed data file: 51_D4_Ets1_WT_IL6.bedGraph.gz


title: Ets1 ChIP-seq [52_D4_Ets1_BATFKO1_IL6]

description:
52_D4_Ets1_BATFKO1_IL6
processed data file: 52_D4_Ets1_BATFKO_IL6.bedGraph.gz


title: Ets1 ChIP-seq [49_D4_Ets1_WT1]

description:
49_D4_Ets1_WT1
processed data file: 49_D4_Ets1_WT.bedGraph.gz


title: CTCF ChIP-seq [43_D4_CTCF_Ets1WT1_IL6]

description:
43_D4_CTCF_Ets1WT1_IL6
processed data file: 47_D4_CTCF_Ets1WT_IL6.bedGraph.gz


title: CTCF ChIP-seq [46_D4_CTCF_Ets1cKO2]

description:
46_D4_CTCF_Ets1cKO2
processed data file: 46_D4_CTCF_Ets1cKO.bedGraph.gz


title: Ets1 ChIP-seq [53_D4_Ets1_WT2]

description:
53_D4_Ets1_WT2
processed data file: 49_D4_Ets1_WT.bedGraph.gz


title: CTCF ChIP-seq [42_D4_CTCF_Ets1cKO1]

description:
42_D4_CTCF_Ets1cKO1
processed data file: 46_D4_CTCF_Ets1cKO.bedGraph.gz


title: CTCF ChIP-seq [44_D4_CTCF_Ets1cKO1_IL6]

description:
44_D4_CTCF_Ets1cKO1_IL6
processed data file: 48_D4_CTCF_Ets1cKO_IL6.bedGraph.gz


title: CTCF ChIP-seq [41_D4_CTCF_Ets1WT1]

description:
41_D4_CTCF_Ets1WT1
processed data file: 45_D4_CTCF_Ets1WT.bedGraph.gz


title: CTCF ChIP-seq [47_D4_CTCF_Ets1WT2_IL6]

description:
47_D4_CTCF_Ets1WT2_IL6
processed data file: 47_D4_CTCF_Ets1WT_IL6.bedGraph.gz


title: Ets1 ChIP-seq [56_D4_Ets1_BATFKO2_IL6]

description:
56_D4_Ets1_BATFKO2_IL6
processed data file: 52_D4_Ets1_BATFKO_IL6.bedGraph.gz


title: CTCF ChIP-seq [45_D4_CTCF_Ets1WT2]

description:
45_D4_CTCF_Ets1WT2
processed data file: 45_D4_CTCF_Ets1WT.bedGraph.gz


title: CTCF ChIP-seq [39_D4_CTCF_BATFKO1_Th17]

description:
39_D4_CTCF_BATFKO1_Th17
processed data file: 39_D4_CTCF_BATFKO_Th17.bedGraph.gz


title: CTCF ChIP-seq [36_D4_CTCF_BATFKO2_IL6]

description:
36_D4_CTCF_BATFKO2_IL6
processed data file: 30_D4_CTCF_BATFKO_IL6.bedGraph.gz


title: CTCF ChIP-seq [38_D4_CTCF_WT2_Th17]

description:
38_D4_CTCF_WT2_Th17
processed data file: 37_D4_CTCF_WT_Th17.bedGraph.gz


title: CTCF ChIP-seq [35_D4_CTCF_WT2_IL6]

description:
35_D4_CTCF_WT2_IL6
processed data file: 29_D4_CTCF_WT_IL6.bedGraph.gz


title: CTCF ChIP-seq [40_D4_CTCF_BATFKO2_Th17]

description:
40_D4_CTCF_BATFKO2_Th17
processed data file: 39_D4_CTCF_BATFKO_Th17.bedGraph.gz


title: CTCF ChIP-seq [34_D4_CTCF_BATFKO2]

description:
34_D4_CTCF_BATFKO2
processed data file: 28_D4_CTCF_BATFKO.bedGraph.gz


title: CTCF ChIP-seq [31_CTCF_Naive_WT2]

description:
31_CTCF_Naive_WT2
processed data file: 25_CTCF_Naive_WT.bedGraph.gz


title: CTCF ChIP-seq [37_D4_CTCF_WT1_Th17]

description:
37_D4_CTCF_WT1_Th17
processed data file: 37_D4_CTCF_WT_Th17.bedGraph.gz


title: CTCF ChIP-seq [29_D4_CTCF_WT1_IL6]

description:
29_D4_CTCF_WT1_IL6
processed data file: 29_D4_CTCF_WT_IL6.bedGraph.gz


title: CTCF ChIP-seq [30_D4_CTCF_BATFKO1_IL6]

description:
30_D4_CTCF_BATFKO1_IL6
processed data file: 30_D4_CTCF_BATFKO_IL6.bedGraph.gz


title: CTCF ChIP-seq [32_CTCF_Naive_BATFKO2]

description:
32_CTCF_Naive_BATFKO2
processed data file: 26_CTCF_Naive_BATFKO.bedGraph.gz


title: CTCF ChIP-seq [26_CTCF_Naive_BATFKO1]

description:
26_CTCF_Naive_BATFKO1
processed data file: 26_CTCF_Naive_BATFKO.bedGraph.gz


title: CTCF ChIP-seq [27_D4_CTCF_WT1]

description:
27_D4_CTCF_WT1
processed data file: 27_D4_CTCF_WT.bedGraph.gz


title: CTCF ChIP-seq [28_D4_CTCF_BATFKO1]

description:
28_D4_CTCF_BATFKO1
processed data file: 28_D4_CTCF_BATFKO.bedGraph.gz


title: CTCF ChIP-seq [25_CTCF_Naive_WT1]

description:
25_CTCF_Naive_WT1
processed data file: 25_CTCF_Naive_WT.bedGraph.gz


title: Med12 ChIP-seq [21_D4_Med12_WT2]

description:
21_D4_Med12_WT2
processed data file: 21_D4_Med12_WT.bedGraph.gz


title: Med12 ChIP-seq [22_D4_Med12_BATFKO2]

description:
22_D4_Med12_BATFKO2
processed data file: 22_D4_Med12_BATFKO.bedGraph.gz


title: Med12 ChIP-seq [17_D4_Med12_WT1]

description:
17_D4_Med12_WT1
processed data file: 21_D4_Med12_WT.bedGraph.gz


title: BATF ChIP-seq [16_BATF_Naive_WT2]

description:
16_BATF_Naive_WT2
processed data file: 16_BATF_Naive_WT.bedGraph.gz


title: Med12 ChIP-seq [20_D4_Med12_BATFKO1_IL6]

description:
20_D4_Med12_BATFKO1_IL6
processed data file: 24_D4_Med12_BATFKO_IL6.bedGraph.gz


title: Med12 ChIP-seq [24_D4_Med12_BATFKO2_IL6]

description:
24_D4_Med12_BATFKO2_IL6
processed data file: 24_D4_Med12_BATFKO_IL6.bedGraph.gz


title: BATF ChIP-seq [15_BATF_Naive_WT1]

description:
15_BATF_Naive_WT1
processed data file: 16_BATF_Naive_WT.bedGraph.gz


title: Med12 ChIP-seq [18_D4_Med12_BATFKO1]

description:
18_D4_Med12_BATFKO1
processed data file: 22_D4_Med12_BATFKO.bedGraph.gz


title: CTCF ChIP-seq [33_D4_CTCF_WT2]

description:
33_D4_CTCF_WT2
processed data file: 27_D4_CTCF_WT.bedGraph.gz


title: BATF ChIP-seq [14_D2_BATF_WT2_Th17]

description:
14_D2_BATF_WT2_Th17
processed data file: 13_D2_BATF_WT_Th17.bedGraph.gz


title: BATF ChIP-seq [13_D2_BATF_WT1_Th17]

description:
13_D2_BATF_WT1_Th17
processed data file: 13_D2_BATF_WT_Th17.bedGraph.gz


title: BATF ChIP-seq [11_D4_BATF_WT2]

description:
11_D4_BATF_WT2
processed data file: 9_D4_BATF_WT.bedGraph.gz


title: BATF ChIP-seq [10_D4_BATF_WT1_IL6]

description:
10_D4_BATF_WT1_IL6
processed data file: 12_D4_BATF_WT_IL6.bedGraph.gz


title: IRF4 ChIP-seq [7_D1_IRF4_WT2]

description:
7_D1_IRF4_WT2
processed data file: 5_D1_IRF4_WT.bedGraph.gz


title: IRF4 ChIP-seq [8_D1_IRF4_WT2_IL6]

description:
8_D1_IRF4_WT2_IL6
processed data file: 6_D1_IRF4_WT_IL6.bedGraph.gz


title: BATF ChIP-seq [9_D4_BATF_WT1]

description:
9_D4_BATF_WT1
processed data file: 9_D4_BATF_WT.bedGraph.gz


title: IRF4 ChIP-seq [6_D1_IRF4_WT1_IL6]

description:
6_D1_IRF4_WT1_IL6
processed data file: 6_D1_IRF4_WT_IL6.bedGraph.gz


title: BATF ChIP-seq [4_D1_BATF_WT2_IL6]

description:
4_D1_BATF_WT2_IL6
processed data file: 2_D1_BATF_WT_IL6.bedGraph.gz


title: BATF ChIP-seq [12_D4_BATF_WT2_IL6]

description:
12_D4_BATF_WT2_IL6
processed data file: 12_D4_BATF_WT_IL6.bedGraph.gz


title: BATF ChIP-seq [1_D1_BATF_WT1]

description:
1_D1_BATF_WT1
processed data file: 1_D1_BATF_WT.bedGraph.gz


title: Med12 ChIP-seq [23_D4_Med12_WT2_IL6]

description:
23_D4_Med12_WT2_IL6
processed data file: 23_D4_Med12_WT_IL6.bedGraph.gz


title: Med12 ChIP-seq [19_D4_Med12_WT1_IL6]

description:
19_D4_Med12_WT1_IL6
processed data file: 23_D4_Med12_WT_IL6.bedGraph.gz


title: Mouse 24 h RPE 2

city: Irvine

first: Les

last: Kallestad

address: 829 Health Sciences Rd

department: Ophthalmology

institute: University of California Irvine

data_processing:
Raw files were aligned using RNA-STAR
Rsubread's featurcounts was used to generate read counts
edgeR was used for DE
R enviroment was used to analyze data
Genome_build: GRCm38.p6 and Panu_3.0
Supplementary_files_format_and_content: csv, raw counts from Rsubread

source_name: Mouse RPE/choroid

extract_protocol:
Retina/RPE was isolated, stored at 4 degress in RNA later or RNA protect, respectively, and RNA was harvested miRNAeasy micro.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: gender

value: Male

value: 30 days

tag: pmi interval

value: RPE/choroid


title: HC2

city: Stanford

first: Olivia

last: Leventhal

state: California (CA)

address: 1201 Welch Road, rm p220

department: Neurology

institute: Stanford University

data_processing:
Real-Time Analysis (RTA) software called RTA2 used for basecalling.
Base call files were demultiplexed using cellranger mkfastq version 3.0.2
RNA-seq reads were mapped alligned to the GRCh38 3.0.0 genome assembly available from 10X Genomics using cellranger count version 3.0.2
Gene expression matrices were generated using cellranger count version 3.0.2
Gene expression matrices for each sample were loaded into the R package 'Seurat' v3.0 and all samples  were merged into one Seurat object
Genome_build: GRCh38 3.0.0
Supplementary_files_format_and_content: tar archive for each sample containing expression matrix, cellbarcodes, and genes

source_name: peripheral blood mononuclear cells

extract_protocol:
TEMRA cells were Live cell sorting using an LSRFortessa (BD Biosciences). See Extended Data Figure 8 for gating strategy. RNA was extracted according to the 10x v2 5' Expression library kit.
Libraries were prepared  according to the 10x v2 5' Expression library kit.

value: blood

value: CD8+ TEMRA cells

tag: diagnosis

value: Healthy


title: HC3


title: AD2

value: AD


title: AD1


title: HC7


title: Mouse 12 h RPE 3


title: Mouse 12 h RPE 2


title: IRF4 ChIP-seq [5_D1_IRF4_WT1]

description:
5_D1_IRF4_WT1
processed data file: 5_D1_IRF4_WT.bedGraph.gz

tag: strain/background

value: wild-type

value: spleen and lymph nodes

value: Activated CD4+ T cells


title: Mouse 6 h RPE 4

value: 6 h


title: Mouse 12 h RPE 1


title: HC6-957

tag: cell type


title: AD4


title: BATF ChIP-seq [3_D1_BATF_WT2]

description:
3_D1_BATF_WT2
processed data file: 1_D1_BATF_WT.bedGraph.gz

value: BATF


title: Mouse 6 h RPE 1


title: MCI2

value: MCI


title: Mouse 6 h RPE 2


title: BATF ChIP-seq [2_D1_BATF_WT1_IL6]

description:
2_D1_BATF_WT1_IL6
processed data file: 2_D1_BATF_WT_IL6.bedGraph.gz

tag: treatment


title: Mouse 6 h RPE 3


title: Mouse 3 h RPE 4

value: 3 h


title: Mouse 3 h RPE 2


title: Mouse 24 h RPE 4


title: Mouse 24 h RPE 3


title: Mouse 1 h RPE 4

value: 1 h


title: Mouse 3 h RPE 1


title: Mouse 24 h RPE 1


title: Mouse 12 h RPE 4


title: Mouse 1 h RPE 2


title: Mouse 1 h RPE 3


title: Mouse 45 min RPE 4

value: 45 min


title: Mouse 45 min RPE 1


title: Mouse 1 h RPE 1


title: Mouse 45 min RPE 3


title: Mouse 3 h RPE 3


title: Mouse 30 min RPE 4

value: 30 min


title: Mouse 30 min RPE 1

value: Male


title: Mouse 15 min RPE 4

value: 30 days

value: 15 min


title: Mouse 30 min RPE 2

value: RPE/choroid


title: Mouse 15 min RPE 1


title: Mouse 0 h RPE 4

value: 0 h


title: Mouse 15 min RPE 3


title: Mouse 0 h RPE 3


title: Mouse 15 min RPE 2


title: Mouse 0 h RPE 2


title: Mouse 0 h RPE 1


title: yw_RNA-seq_rep3

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

data_processing:
ChIP-seq: The ChIP-seq samples were mapped to the Drosophila melanogaster (dm3) genome assembly using Bowtie2 with the default parameters, after the adaptor trimming by Trimmomatic.  For each of the four factors, the peak calling was performed by the ChIP-seq reads of wt or a mutant condition to its own mutant ChIP or IgG or Input. The peaks were called using MACS2 (Zhang et al. 2008) with default parameters and the confident peaks were determined by an FDR < 1%. The peaks overlapped with Drosophila blacklist were also removed.
ChIP-nexus: Before aligning the ChIP-nexus reads to the genome, the 5’ fixed barcode (1-5) was first removed and the random 4nt barcode was retained for each read. After the 3’ adaptor trimming by Trimmomatic, the sequencing reads were collapsed to only include unique reads. The random 4nt barcode was further removed and the reads with at least 22nt were retained for mapping. We mapped the reads using bowtie with the parameter setting “-k 1 -m 1 -v 2 --best --strata”. Similar to the ChIP-seq data, the ChIP-nexus peak calling was performed by MACS2 using the default parameter.
PRO-seq: The adaptors were first trimmed from the sequencing reads by cutadapt software and the reads with at least 15 nt were retained.  We then removed reads that mapped to rRNAs and the remaining reads were further mapped to the Drosophila melanogaster (dm3) genome assembly using BWA with the default parameters.
RNA-seq: After trimming the adaptor sequences using Trimmomatic, for each factor, the RNA-seq reads from the replicated wild type (x3) and mutant samples (x3) were mapped to the Drosophila melanogaster (dm3) genome assembly genome assembly using HISAT2.
Genome_build: dm3
Supplementary_files_format_and_content: bigwig for coverage, bigbed for ChIP-seq/ChIP-nexus peak calls, RNA-seq #reads per gene in xlsx.

organism: Drosophila melanogaster

source_name: Drosophila early embryo

growth_protocol: Drosophila embryos were aged to 2-4 hours at 25 degrees and collected

extract_protocol:
Standard protocols were used to make chromatin extract for ChIP. Total RNAs were extracted with Trizol reagent for RNA-seq. Standard PRO-seq protocol was used to make PRO-seq libraries
ChIP-seq libraries were made using NEB DNA library prep kit. ChIP-nexus library was made as previouly described (He, et al ,2015). RNA-seq libraries were made by using illumina True-seq total RNA library kit LT. PRO-seq libraries were made as previously described (Kwak, et al, 2013).

value: yw

value: early embyro

value: 2-4 hours

tag: molecule subtype

value: Total RNA


title: yw_RNA-seq_rep1

tag: tissue


title: Mouse 24 h retina 3

source_name: Mouse retina

value: retina


title: yw_RNA-seq_rep2


title: insv_RNA-seq_rep3

value: insv mutant


title: Mouse 24 h retina 4


title: insv_RNA-seq_rep2


title: Mouse 24 h retina 1


title: Mouse 30 min RPE 3


title: insv_RNA-seq_rep1


title: Mouse 45 min RPE 2


title: elba3_RNA-seq_rep3

value: elba3 mutant


title: elba3_RNA-seq_rep2


title: Mouse 12 h retina 3


title: elba3_RNA-seq_rep1


title: Mouse 12 h retina 4


title: Mouse 12 h retina 2


title: Mouse 12 h retina 1


title: Mouse 6 h retina 4

value: 6 h


title: elba2_RNA-seq_rep3

value: elba2 mutant


title: elba2_RNA-seq_rep1


title: Mouse 6 h retina 2


title: Mouse 3 h retina 4

value: 3 h


title: Mouse 6 h retina 1


title: elba2_RNA-seq_rep2


title: Mouse 24 h retina 2


title: elba1_RNA-seq_rep1

value: elba1 mutant


title: Mouse 3 h retina 2


title: elba1_RNA-seq_rep3


title: Mouse 6 h retina 3


title: yw_Pro-seq_rep2

data_processing:
Library strategy: PRO-seq
ChIP-seq: The ChIP-seq samples were mapped to the Drosophila melanogaster (dm3) genome assembly using Bowtie2 with the default parameters, after the adaptor trimming by Trimmomatic.  For each of the four factors, the peak calling was performed by the ChIP-seq reads of wt or a mutant condition to its own mutant ChIP or IgG or Input. The peaks were called using MACS2 (Zhang et al. 2008) with default parameters and the confident peaks were determined by an FDR < 1%. The peaks overlapped with Drosophila blacklist were also removed.
ChIP-nexus: Before aligning the ChIP-nexus reads to the genome, the 5’ fixed barcode (1-5) was first removed and the random 4nt barcode was retained for each read. After the 3’ adaptor trimming by Trimmomatic, the sequencing reads were collapsed to only include unique reads. The random 4nt barcode was further removed and the reads with at least 22nt were retained for mapping. We mapped the reads using bowtie with the parameter setting “-k 1 -m 1 -v 2 --best --strata”. Similar to the ChIP-seq data, the ChIP-nexus peak calling was performed by MACS2 using the default parameter.
PRO-seq: The adaptors were first trimmed from the sequencing reads by cutadapt software and the reads with at least 15 nt were retained.  We then removed reads that mapped to rRNAs and the remaining reads were further mapped to the Drosophila melanogaster (dm3) genome assembly using BWA with the default parameters.
RNA-seq: After trimming the adaptor sequences using Trimmomatic, for each factor, the RNA-seq reads from the replicated wild type (x3) and mutant samples (x3) were mapped to the Drosophila melanogaster (dm3) genome assembly genome assembly using HISAT2.
Genome_build: dm3
Supplementary_files_format_and_content: bigwig for coverage, bigbed for ChIP-seq/ChIP-nexus peak calls, RNA-seq #reads per gene in xlsx.

value: RNAPolII run-on RNA


title: yw_Pro-seq_rep1


title: Mouse 3 h retina 1

value: Male


title: Mouse 1 h retina 4

value: 30 days

value: 1 h


title: insv_Pro-seq_rep1


title: Mouse 1 h retina 3


title: elba3_Pro-seq_rep2


title: Mouse 1 h retina 2


title: Mouse 1 h retina 1


title: Mouse 45 min retina 4

value: 45 min


title: elba1_RNA-seq_rep2


title: elba2_Pro-seq_rep1


title: Mouse 3 h retina 3


title: elba1_Pro-seq_rep1


title: elba1_Pro-seq_rep2


title: elba3_Pro-seq_rep1


title: Mouse 45 min retina 1


title: wtInsv_ChiP-Nexus

value: ChIPed genomic DNA

tag: antibody

value: Insv antibody in ChIP


title: Mouse 30 min retina 3

tag: age

value: 30 min


title: Mouse 45 min retina 2


title: wtElba3_ChiP-Nexus

value: yw

value: early embyro

value: 2-4 hours

value: Elba3 antibody in ChIP


title: Mouse 30 min retina 4

value: retina


title: Mouse 30 min retina 1


title: Mouse 30 min retina 2


title: insv_Pro-seq_rep2

value: insv mutant


title: wtElba2_ChiP-Nexus

value: Elba2 antibody in ChIP


title: wtElba1_ChiP-Nexus

value: Elba1 antibody in ChIP


title: wt_Input

value: Input control in ChIP


title: elba3_Input

value: elba3 mutant


title: Mouse 15 min retina 4

value: Male

value: 15 min


title: Mouse 15 min retina 2

value: 30 days


title: insv_Input


title: Mouse 15 min retina 3


title: Mouse 45 min retina 3

value: 45 min


title: Mouse 15 min retina 1


title: wtIgG_ChiP-seq

value: ChIPed genomic DNA

value: IgG control in ChIP


title: elba2_Input

value: elba2 mutant


title: Mouse 0 h retina 4

value: 0 h


title: Mouse 0 h retina 3


title: insvIgG_ChiP-seq

value: early embyro


title: elba2_Pro-seq_rep2

value: 2-4 hours

value: RNAPolII run-on RNA


title: Mouse 0 h retina 2

value: retina


title: elba1IgG_ChiP-seq

value: elba1 mutant